Progression through developmental stages requires complex interactions of transcription factors and regulatory elements to achieve correct temporal and spatial patterns of requisite gene expression. Biochemical and genetic studies have implicated epigenetic modifications of chromatin structure as an important mechanism in regulation of gene transcription. Alteration of nucleosome conformation and/or position (termed chromatin remodeling) within gene regulatory elements serves to promote or restrict gene expression through regulating accessibility of trans-acting transcription factors. Mechanistically, modification of local chromatin structure is achieved, in part, through the activity of multi-subunt protein complexes that utilize the energy of ATP hydrolysis to disrupt nucleosome conformation and position. One important class of mammalian ATP- dependent nucleosome remodelers is that of the SWI/SNF-related family, which consists of large, multi-protein complexes that utilize either brahma (BRM) or brahma-related gene 1 (BRG1) as the catalytic subunit. Biochemical studies on the human SWI-SNF- related complexes and its yeast counterpart have demonstrated the ability of these complexes to disrupt histone-DNA contacts and reposition nucleosomes in an ATP- dependent manner. Mammalian SWI/SNF complexes can be grouped into two major subfamilies, BAF (Brahma-related-gene 1 (BRG1)-associated factor) and PBAF (polybromo-associated BAF). Although the BAF/PBAF complexes share many common subunits; they are distinguishable by the presence of different ARID DNA binding subunits. Preliminary data suggest that these variant complexes exist in a delicate balance with each other, and upon loss of one complex, large-scale reorganization of the chromatin-remodeling machinery occurs. A series of experiments are proposed to study how these complexes interact with one another and with the genome on a global scale. Such an approach is critical to address how the balance of chromatin remodeling complexes contributes to a stable system of gene expression and how loss of this balance contributes to developmental abnormalities and disease.